Monomethyl Histone H3 Lysine 4 as an Epigenetic Mark for Silenced Euchromatin in Chlamydomonas  

Abstract

Histone Lys methylation plays an important role in determining chromatin states and is mostly catalyzed by SET domaincontaining proteins. The outcome, transcriptional repression or activation, depends on the methylated histone residue, the degree of methylation, and the chromatin context. Dimethylation or trimethylation of histone H3 Lys 4 (H3K4me2 or H3K4me3) has been correlated with transcriptionally competent/active genes. However, H3K4 methylation has also been implicated in gene silencing. This dualistic nature of the H3K4 methyl mark has thus far remained unresolved. In the green alga Chlamydomonas reinhardtii, Mut11p, related to a subunit of trithorax-like methyltransferase complexes, is required for transcriptional silencing. Here, we show that Mut11p interacts with conserved components of H3K4 methyltransferase machineries, and an affinity-purified Mut11p complex(es) methylates histones H3, H2A, and H4. Moreover, a Mut11 mutant showed global loss of monomethylated H3K4 (H3K4me1) and an increase in dimethylated H3K4. By chromatin immunoprecipitation analysis, this strain also displayed substantial reduction in H3K4me1 and enrichment in H3K4me2 associated with transcriptionally derepressed genes, transgenes, and retrotransposons. RNA interference-mediated suppression of Set1, encoding an H3K4 methyltransferase, induced similar phenotypes, but of lower magnitude, and no detectable increase in H3K4me2. Together, our results suggest functional differentiation between dimethyl H3K4 and monomethyl H3K4, with the latter operating as an epigenetic mark for repressed euchromatin.

MLL5, a trithorax homolog, indirectly regulates H3K4 methylation, represses cyclin A2 expression, and promotes myogenic differentiation

“…In general, H3K4-2Me and H3K4-3Me at transcriptional start sites increase accessibility and correlate with activation, whereas monomethylation correlates with repression (31). However, in MLL5 knockdown cells, elevated CCRE activity correlates with decreased H3K4-2Me but may result from reduced recruitment of repressors, Brm/Brg.…”

“…3F), supporting an indirect mechanism for the altered global H3K4 methylation. H3K4 dimethylation and trimethylation usually correlate with increased transcription when present at the 5Ј ends of genes, but monomethylation of Lys-4 correlates with repressive euchromatin (31). ChIP analysis of the CCRE and an upstream CycA promoter site (Ϫ573) revealed a Ϸ2-fold decrease in H3K4-2Me levels in MLL5 knockdown cells (Fig.…”

Histone H3 phosphorylation: Universal code or lineage specific dialects?

“…51 Based on chromatin immunoprecipitation assays, both H3T3ph and H3K4me1 associate with silent chromatin and their distribution appears to be mutually exclusive with that of the activating di or trimethyl forms of H3K4. 51,52 It is tempting to speculate, by analogy to the proposed function of H3T11ph, that H3T3ph may promote the recruitment and/or the activity of a demethylase that erases the H3K4me3 and H3K4me2 states. MUT9, the kinase responsible for H3T3 phosphorylation in C. reinhardtii, seems to have evolved in the plant lineage and lacks metazoa orthologs (Fig.…”

Unstable RNAi Effects Through Epigenetic Silencing of an Inverted Repeat Transgene in Chlamydomonas reinhardtii

“…In some eukaryotes including C. reinhardtii, monomethylation of lysine 4 in histone H3 (H3K4) and monomethylation of H3K9 are putative epigenetic markers for a transcriptionally silent/inactive chromatin state (Cheung and Lau 2005;Van Dijk et al 2005;Waterborg et al 1995;Casas-Mollano et al 2007;Pfluger and Wagner 2007), and the underlying DNA in heterochromatin is often accompanied by methylation. In contrast, histones located in euchromatic regions usually have different types of modifications, such as acetylation, and the DNA in these regions is usually not highly methylated.…”